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OPENSEQ.org
3r9j_C_A
Genes: A B A+B
Length: 77 260 311
Sequences: 738 15241 598
Seq/Len: 9.58 58.62 1.92
MirrorTree (Pazo et al. 2001) 0.77
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.10 0.02 1.77
2 0.10 0.03 1.77
5 0.10 0.03 1.77
10 0.10 0.05 1.77
20 0.10 0.06 1.77
100 0.10 0.11 1.80
∞ 0.10 0.18 1.81
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
15_V 236_G 1.55 0.92 0.51
15_V 4_I 1.47 0.89 0.45
17_E 150_V 1.24 0.75 0.26
13_N 37_I 1.17 0.69 0.21
16_A 192_D 1.15 0.67 0.20
33_K 37_I 1.09 0.61 0.17
3_T 4_I 1.09 0.61 0.16
5_N 116_F 1.08 0.59 0.16
68_V 19_S 1.06 0.57 0.15
15_V 79_R 1.03 0.54 0.13
26_H 72_Q 1.01 0.53 0.12
49_M 197_E 1.01 0.53 0.12
28_L 76_K 1.01 0.52 0.12
46_D 79_R 1.01 0.52 0.12
7_A 147_V 1.01 0.52 0.12
14_I 150_V 1.00 0.52 0.12
32_R 34_T 1.00 0.51 0.12
43_V 7_V 0.98 0.49 0.11
56_Q 164_S 0.96 0.47 0.10
16_A 206_K 0.94 0.44 0.09
14_I 130_L 0.93 0.44 0.09
15_V 237_K 0.93 0.44 0.09
21_S 23_I 0.93 0.44 0.09
31_L 61_V 0.93 0.43 0.09
61_I 253_F 0.93 0.43 0.09
26_H 116_F 0.92 0.42 0.09
18_R 242_T 0.91 0.41 0.08
66_L 102_V 0.91 0.41 0.08
50_V 208_V 0.90 0.40 0.08
32_R 199_V 0.89 0.39 0.08
54_L 110_K 0.89 0.39 0.08
8_K 79_R 0.89 0.39 0.08
18_R 17_T 0.89 0.39 0.08
39_I 156_I 0.88 0.38 0.07
29_P 52_C 0.88 0.38 0.07
4_A 23_I 0.88 0.38 0.07
39_I 50_M 0.87 0.37 0.07
52_V 138_E 0.87 0.37 0.07
62_S 246_L 0.86 0.36 0.07
46_D 61_V 0.86 0.36 0.07
62_S 22_A 0.86 0.36 0.07
2_N 236_G 0.86 0.36 0.07
66_L 48_L 0.86 0.36 0.07
60_D 130_L 0.86 0.36 0.07
15_V 221_S 0.85 0.35 0.07
17_E 39_F 0.85 0.35 0.07
16_A 64_I 0.84 0.34 0.06
4_A 199_V 0.84 0.34 0.06
41_K 64_I 0.84 0.34 0.06
30_Q 140_I 0.84 0.34 0.06
68_V 7_V 0.83 0.34 0.06
21_S 61_V 0.83 0.33 0.06
17_E 223_Q 0.83 0.33 0.06
55_E 7_V 0.83 0.33 0.06
13_N 217_V 0.82 0.32 0.06
52_V 227_V 0.82 0.32 0.06
6_I 215_Q 0.82 0.32 0.06
62_S 219_R 0.82 0.32 0.06
34_D 23_I 0.82 0.32 0.06
29_P 65_Q 0.81 0.31 0.06
40_C 37_I 0.81 0.31 0.06
12_Q 7_V 0.81 0.31 0.05
61_I 201_E 0.81 0.31 0.05
12_Q 217_V 0.80 0.30 0.05
55_E 3_R 0.80 0.30 0.05
12_Q 121_S 0.80 0.30 0.05
43_V 36_V 0.80 0.30 0.05
8_K 121_S 0.80 0.30 0.05
9_E 147_V 0.80 0.30 0.05
62_S 19_S 0.80 0.30 0.05
21_S 229_L 0.79 0.29 0.05
71_P 89_S 0.79 0.29 0.05
28_L 177_H 0.78 0.29 0.05
72_E 195_S 0.78 0.28 0.05
55_E 156_I 0.78 0.28 0.05
62_S 87_P 0.78 0.28 0.05
56_Q 37_I 0.78 0.28 0.05
34_D 180_L 0.78 0.28 0.05
67_N 140_I 0.78 0.28 0.05
28_L 50_M 0.77 0.28 0.05
40_C 162_S 0.77 0.28 0.05
35_I 227_V 0.77 0.27 0.05
23_A 199_V 0.76 0.27 0.04
37_E 35_V 0.76 0.27 0.04
67_N 207_L 0.76 0.27 0.04
71_P 211_I 0.76 0.27 0.04
3_T 179_L 0.76 0.27 0.04
15_V 27_L 0.76 0.26 0.04
8_K 60_F 0.76 0.26 0.04
34_D 211_I 0.75 0.26 0.04
17_E 148_S 0.75 0.26 0.04
65_E 49_I 0.75 0.26 0.04
54_L 74_L 0.75 0.26 0.04
14_I 202_I 0.75 0.26 0.04
2_N 103_A 0.75 0.26 0.04
25_P 236_G 0.75 0.25 0.04
60_D 89_S 0.74 0.25 0.04
54_L 178_L 0.74 0.25 0.04
51_T 156_I 0.74 0.25 0.04
33_K 115_E 0.73 0.24 0.04
36_L 29_Q 0.73 0.24 0.04
4_A 48_L 0.73 0.24 0.04
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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